Ph.D Thesis

Ph.D StudentTzunz-Henig Noa
SubjectTranscriptional Profiling and Pathway Analysis of Response
to Interferon-Beta in Immune Cells and Multiple
DepartmentDepartment of Medicine
Supervisors PROF. Ariel Miller
PROF. Ron Pinter
Full Thesis textFull thesis text - English Version


Multiple Sclerosis (MS) is an autoimmune disorder of the central nervous system with T cells, monocytes and B cells shown to be involved in its pathophysiology. Interferon β (IFN-β) is widely used immunomodulator drug for treating MS. In this study we characterized the transcriptional response of monocytes to IFN-β in order to identify novel, cell-specific IFN-β functions and pathways. We looked for perturbations in the IFN signaling in monocytes from MS patients compared to healthy controls, and tested the hypothesis that altered stability of transcripts affects the clinical response to IFN-β treatment.

Using Illumina microarrays, we compared the gene expression profiles of monocytes and T cells in response to in-vitro priming with TNF-α and overnight IFN-β stimulation. Many of the differentially expressed genes (DEGs) in the IFN-β-exposed monocytes were involved in immune functions, cell migration, and protein translation. Network and pathway analysis of the IFN-β-exposed monocytes revealed pathways that had not been previously described in connection to IFN-β response, such as the high-mobility group box-1 (HMGB1) signaling pathway. However, most DEGs in the IFN-β-exposed monocytes did not cluster to known networks or canonical pathways, suggesting a different mechanism of transcription regulation by IFN-β in monocytes.

Based on these findings and the important role of monocytes in MS, we compared the expression profiles of monocytes from MS patients versus healthy controls after in-vitro IFN-b induction. We found the expression profiles to be highly similar, with 80% of the DEGs common to both groups. Only a few DEGs were highlighted, such as PADI4 and CX3CR1, which were previously recognized in the context of MS. Few other genes, such as RNF130, were novel.

To study an additional pharmacogenetic aspect of IFN-β response we used lymphoblastoid cell lines (LCLs) derived from MS patients with defined clinical response phenotype. We hypothesized that altered stability of transcripts may partially affect the clinical response of patients to IFN-b. The RNA degradation rates of 9 transcripts were compared between good and poor responders. Two transcripts, IL15RA and IRF7, showed statistically significant differences in the decay rates, supporting our hypothesis.

We demonstrated in this study that the monocyte response to IFN-β is distinct from the T cell response and involves novel IFN-β response genes and pathways. This also emphasizes the importance of cell-specific datasets for elucidating the spectrum of cytokine-mediated effects, and contributes to the understanding of the regulatory effects of IFN-β.